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Most Cisco platforms don't directly support per-user/per-session rate limiting unless you define a policy for each user's IPs (which is a possible solution if we're only dealing with a hundred or so users).
6500s offer Microflow policing, which if you have that hardware, might be an option.
PS:
BTW, a possible alternative might be to use QoS to deprioritize FTP traffic to/from your DC FTP servers. Such a QoS policy allows such traffic to use all available bandwidth, but such consumption won't be adverse to more critical traffic.
